2AL0

Crystal structure of nitrophorin 2 ferrous aqua complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PEE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.65	24.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.405	α = 90
b = 34.405	β = 90
c = 255.181	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	bent Si-mirror	2004-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9000	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	23	97	0.05	21	4.8	21168	21168			28.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	97		0.23	2.6	3.8	2039

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1PEE	1.6	23	19970	19970	1084	97.27	0.18449	0.18449	0.18212	0.22927	RANDOM	19.075

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.2			-0.2		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.081
r_dihedral_angle_3_deg	13.016
r_dihedral_angle_1_deg	7.134
r_scangle_it	3.988
r_dihedral_angle_4_deg	3.196
r_scbond_it	3.085
r_mcangle_it	2.025
r_angle_refined_deg	1.893
r_mcbond_it	1.75
r_angle_other_deg	0.923
r_mcbond_other	0.361
r_symmetry_vdw_refined	0.288
r_nbd_refined	0.227
r_symmetry_vdw_other	0.197
r_symmetry_hbond_refined	0.197
r_nbd_other	0.182
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.125
r_nbtor_other	0.086
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1434
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
d*TREK	data scaling